The river is known to have 24 tributaries that include: Western Creek, Warrawanda Creek, Shovelanna Creek, Kalgan Creek, Fortescue River South, Cowcumba Creek, Macklin Creek and Tanga Tanga Creek.

During Cyclone Joan in 1975 many of these tributaries also flooded. Weeli Wolli Creek and Weelumurra Creek both overflowed and caused floods and washaways on the Hamersley Iron and Mount Newman railway lines.[5]

The river flows through a number of permanent water pools on the latter part of its journey including Tarda Pool, Mungowarra Pool, Crossing Pool and Deep Reach Pool.

The Fortescue Catchment area drains from the southern side of the Chichester Plateau and the northern side of the Hamersley Range making use of the trough between the two. The valley plains are composed of earthy clays with some cracking clays, loams and hard red soils.

Water is stored at Ophthalmia Dam which holds a total volume of 32,000ML, and a total of 6,290 ML/year are drawn from the surface water for use in the town of Newman.[6]

The headwaters area of Fortescue River is flat and marshy. It is a location where Western Creek, Warrawanda Creek and Fortescue River converge.

The river then flows through a poorly defined channel as far as Gregory Gorge,[7] when the river starts to form a well defined channel. It then flows through a number of pools before reaching the estuarine area.[8]

The mouth of the river is a large estuarine area. The estuary is mostly unmodified, and functions primarily as a result of river energy. The delta formed by the river is tide dominated.
The estuary covers a total surface area of 23.3 square kilometres (9 sq mi)[9]
The majority of the estuarine area is made up of salt marsh and intertidal flats. A colony of mangroves use the estuary as habitat and occupy an area of 1.2 square kilometres (0 sq mi). Large female Barramundi are known to inhabit the estuary.